7B2M

Cryo-EM structure of complement C4b in complex with nanobody E3


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.39 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Multifaceted Activities of Seven Nanobodies against Complement C4b.

De la O Becerra, K.I.Oosterheert, W.van den Bos, R.M.Xenaki, K.T.Lorent, J.H.Ruyken, M.Schouten, A.Rooijakkers, S.H.M.van Bergen En Henegouwen, P.M.P.Gros, P.

(2022) J Immunol 208: 2207-2219

  • DOI: https://doi.org/10.4049/jimmunol.2100647
  • Primary Citation of Related Structures:  
    7B2M, 7B2P, 7B2Q

  • PubMed Abstract: 

    Cleavage of the mammalian plasma protein C4 into C4b initiates opsonization, lysis, and clearance of microbes and damaged host cells by the classical and lectin pathways of the complement system. Dysregulated activation of C4 and other initial components of the classical pathway may cause or aggravate pathologies, such as systemic lupus erythematosus, Alzheimer disease, and schizophrenia. Modulating the activity of C4b by small-molecule or protein-based inhibitors may represent a promising therapeutic approach for preventing excessive inflammation and damage to host cells and tissue. Here, we present seven nanobodies, derived from llama ( Lama glama ) immunization, that bind to human C4b ( Homo sapiens ) with high affinities ranging from 3.2 nM to 14 pM. The activity of the nanobodies varies from no to complete inhibition of the classical pathway. The inhibiting nanobodies affect different steps in complement activation, in line with blocking sites for proconvertase formation, C3 substrate binding to the convertase, and regulator-mediated inactivation of C4b. For four nanobodies, we determined single-particle cryo-electron microscopy structures in complex with C4b at 3.4-4 Å resolution. The structures rationalize the observed functional effects of the nanobodies and define their mode of action during complement activation. Thus, we characterized seven anti-C4b nanobodies with diverse effects on the classical pathway of complement activation that may be explored for imaging, diagnostic, or therapeutic applications.


  • Organizational Affiliation

    Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, the Netherlands.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Complement C4 beta chain656Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P0C0L4 (Homo sapiens)
Explore P0C0L4 
Go to UniProtKB:  P0C0L4
PHAROS:  P0C0L4
GTEx:  ENSG00000244731 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C0L4
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Complement C4 alpha chain767Homo sapiensMutation(s): 1 
UniProt & NIH Common Fund Data Resources
Find proteins for P0C0L4 (Homo sapiens)
Explore P0C0L4 
Go to UniProtKB:  P0C0L4
PHAROS:  P0C0L4
GTEx:  ENSG00000244731 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C0L4
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Complement C4 gamma chain291Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P0C0L4 (Homo sapiens)
Explore P0C0L4 
Go to UniProtKB:  P0C0L4
PHAROS:  P0C0L4
GTEx:  ENSG00000244731 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C0L4
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Anti-C4b nanobody E3135Lama glamaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.39 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTPHENIX1.18.2-3874

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Consejo Nacional de Ciencia y Tecnologia (CONACYT)Mexico604718

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-02
    Type: Initial release
  • Version 1.1: 2022-04-27
    Changes: Database references
  • Version 1.2: 2022-05-04
    Changes: Database references